PXD053582 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Protein misfolding involving entanglements provides a structural explanation for the origin of stretched-exponential refolding kinetics |
Description | Stretched-exponential protein refolding kinetics, first observed decades ago, were attributed to a nonnative ensemble of structures with parallel, non-interconverting folding pathways. However, the structural origin of the large energy barriers preventing interconversion between these folding pathways is unknown. Here, we combine simulations with limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS) to study the protein phosphoglycerate kinase (PGK). Simulations recapitulate its stretched-exponential folding kinetics and reveal that misfolded states involving changes of entanglement underlie this behavior: either formation of a nonnative, noncovalent lasso entanglement or failure to form a native entanglement. These misfolded states act as kinetic traps, requiring extensive unfolding to escape, which results in a distribution of free energy barriers and pathway partitioning. Using LiP-MS and XL-MS, we propose heterogeneous structural ensembles consistent with these data that represent the potential long-lived misfolded states PGK populates. This structural and energetic heterogeneity creates a hierarchy of refolding timescales, explaining stretched-exponential kinetics. |
HostingRepository | PRIDE |
AnnounceDate | 2025-03-18 |
AnnouncementXML | Submission_2025-03-17_18:33:22.130.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Yingzi Xia |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | carbamoylated residue; acetylated residue; monohydroxylated residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-07-02 17:23:27 | ID requested | |
⏵ 1 | 2025-03-17 18:33:22 | announced | |
Publication List
Jiang Y, Xia Y, Sitarik I, Sharma P, Song H, Fried SD, O'Brien EP, Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics. Sci Adv, 11(11):eads7379(2025) [pubmed] |
10.1126/sciadv.ads7379; |
Keyword List
submitter keyword: folding, crosslinking mass spectrometry, stretched-exponential kinetics |
Contact List
Stephen Fried |
contact affiliation | Assistant Professor, Department of Chemistry Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy) |
contact email | sdfried@jhu.edu |
lab head | |
Yingzi Xia |
contact affiliation | Johns Hopkins University |
contact email | yxia39@jhu.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD053582
- Label: PRIDE project
- Name: Protein misfolding involving entanglements provides a structural explanation for the origin of stretched-exponential refolding kinetics